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The Great Civil War was a civil war fought on Skaro between the Daleks loyal to the Dalek Emperor, and Daleks who had been implanted with the Human Factor.
The war was instigated when the Doctor implanted the Human Factor into a group of Daleks who became friendly to the Doctor and whom the Time Lord named Alpha, Beta and Omega. The Doctor tricked the Emperor into sending more Daleks into the machine which the Emperor believed would implant the Dalek Factor into the Daleks and thus eliminate the threat. Instead, the machine implanted the Human Factor. Those Daleks who passed through the machine turned on the Emperor and a battle broke out.
The fighting spread into the throne room amid the Emperor's protests and declarations. The Emperor himself was destroyed, although a blinking light on his casing may have indicated his survival.
The Dalek City was devastated by the conflict and began to explode. The Doctor believed this battle to be the Daleks' final end. (DW: The Evil of the Daleks)
Behind the scenes
The name "Great Civil War" was used to refer to the conflict in REF: Aliens and Enemies, which also referred to the Last Great Time War as the "Great Time War", so that book's accuracy is questionable.